+Open data
-Basic information
Entry | Database: PDB / ID: 7nvj | ||||||
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Title | Crystal structure of UFC1 Y110A & F121A | ||||||
Components | Ubiquitin-fold modifier-conjugating enzyme 1 | ||||||
Keywords | LIGASE / Ubiquitin fold conjugating enzyme 1 (UFC1) / Ufmylation / Y110A / F121A | ||||||
Function / homology | Function and homology information UFM1 conjugating enzyme activity / UFM1 transferase activity / protein ufmylation / protein K69-linked ufmylation / reticulophagy / response to endoplasmic reticulum stress / brain development / extracellular exosome / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Manoj Kumar, P. / Padala, P. / Isupov, M.N. / Wiener, R. | ||||||
Funding support | Israel, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis for UFM1 transfer from UBA5 to UFC1. Authors: Kumar, M. / Padala, P. / Fahoum, J. / Hassouna, F. / Tsaban, T. / Zoltsman, G. / Banerjee, S. / Cohen-Kfir, E. / Dessau, M. / Rosenzweig, R. / Isupov, M.N. / Schueler-Furman, O. / Wiener, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nvj.cif.gz | 50.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nvj.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7nvj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nvj_validation.pdf.gz | 440.3 KB | Display | wwPDB validaton report |
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Full document | 7nvj_full_validation.pdf.gz | 442 KB | Display | |
Data in XML | 7nvj_validation.xml.gz | 9 KB | Display | |
Data in CIF | 7nvj_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/7nvj ftp://data.pdbj.org/pub/pdb/validation_reports/nv/7nvj | HTTPS FTP |
-Related structure data
Related structure data | 7nvkC 7nw1C 2z6pS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19375.254 Da / Num. of mol.: 1 / Mutation: Y110A, F121A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UFC1, CGI-126, HSPC155 / Plasmid: pET32A / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: Q9Y3C8 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 2M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 23, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→33.24 Å / Num. obs: 8491 / % possible obs: 99.8 % / Redundancy: 1.2 % / Biso Wilson estimate: 25.44 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.153 / Net I/σ(I): 13.33 |
Reflection shell | Resolution: 2.2→2.279 Å / Redundancy: 1.1 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 804 / CC1/2: 0.47 / Rrim(I) all: 0.71 / % possible all: 99.14 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Z6P Resolution: 2.2→33.24 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.2 / SU ML: 0.197 / Cross valid method: FREE R-VALUE / ESU R: 0.317 / ESU R Free: 0.228 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.854 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→33.24 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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